<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Hervé,<div><br></div><div>Thanks for your email.</div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;"><br></span></div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">In previous releases, genes on patches were projected from their scaffold sequences (e.g. HSCHR6_MHC_APD_CTG1) and stored onto chromosome-based sequences (e.g. CHR_HSCHR6_MHC_APD_CTG1). Therefore in this case, the gene(s) on this example patch had been projected onto a sequence with coordinate positions in the context of human chromosome 6. Historically, the Ensembl Core Perl API was built to support genes on patches based on these chromosome-based sequences, which were ultimately used to visualise a given patch on the Ensembl Browser with all its associated features.</span></div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;"><br></span></div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">As you mentioned, this has changed as of Release 110 so that we now keep the genes (and their associated features) on their original scaffold patch sequence. I should also clarify that this work only relates to human.</span></div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;"><br></span></div><div><span style="color: rgb(29, 28, 29); orphans: 2; white-space: pre-wrap; widows: 2;">Please do let us know if you have any more questions on this topic.</span></div><div><br></div><div>Thanks and best wishes,</div><div>Natalie</div><div><br><div>
<meta charset="UTF-8"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><div dir="auto" style="caret-color: rgb(0, 0, 0); color: rgb(0, 0, 0); letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;"><b>Natalie Willhöft (Dawson)</b><br>Ensembl Infrastructure Team<br>EMBL-EBI <br>nwillhoft@ebi.ac.uk</div></div>
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<div><br><blockquote type="cite"><div>On 23 Aug 2023, at 06:30, Hervé Pagès <hpages.on.github@gmail.com> wrote:</div><br class="Apple-interchange-newline"><div>
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<div text="#000000" bgcolor="#f6f5f4"><p>Hi,</p><p>Looks like starting with Ensembl 110 (now based on GRCh38.p14),
human gene ENSG00000231116 (VARS) is now reported to be located on
sequence HSCHR6_MHC_APD_CTG1 after being reported to be on
sequence CHR_HSCHR6_MHC_APD_CTG1 for many years (at least since
Ensembl release 85, based on GRCh38.p7).</p><p>Anybody knows what sequence CHR_HSCHR6_MHC_APD_CTG1 was actually
supposed to be? Was never a valid GRCh38 sequence name. At least
the new sequence name belongs to GRCh38.</p><p>Thanks,</p><p>H.<br>
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<pre class="moz-signature" cols="72">--
Hervé Pagès
Bioconductor Core Team
<a class="moz-txt-link-abbreviated" href="mailto:hpages.on.github@gmail.com">hpages.on.github@gmail.com</a>
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